You can just do the subquery in perl first:

my $min_phone_ids = $dbh->selectcol_arrayref("SELECT MIN(PhoneNumberID
+) FROM phone_numbers GROUP BY MemberID");
my $sql = <<EOF;
SELECT FirstName, LastName, PhoneNumber, members.MemberID AS MemberID
FROM members
LEFT JOIN phone_numbers ON 
  members.MemberID=phone_numbers.MemberID
EOF
$sql .= " AND phone_numbers.PhoneNumberID IN ("  . join(',','?' x @$mi
+n_phone_ids). ") "
$sql .= <<EOF;
  WHERE Verified=1
  ORDER BY LastName, FirstName, members.MemberID
EOF
$dbh->selectall_arrayref( $sql, {}, @$min_phone_ids );
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is your join logic correct? As i read it you're checking if the phone id is the same as the min for _any_ member, and not necessarily the min for _that_ member...